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Multiple enhancements and bugfixes#164

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jscaber wants to merge 45 commits intomastercgat-developers/cgat-flow:masterfrom JS-exomecgat-developers/cgat-flow:JS-exomeCopy head branch name to clipboard

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Commits

Commits on Feb 10, 2022

• remove scriptsdir

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• remove scriptsdir

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Commits on Feb 14, 2022

• substatial changes to exome pipeline - bringing it in line with pipeline bamstats and changes in gatk

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• remove mappingqc from pipeline_mapping.py

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• remove mappingqc from pipeline_windows.py

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• remove mappingqc from pipeline peakcalling

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• remove mappingqc from rnaseqqc pipelin

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• remove mappingqc from exome cancer pipeline

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• remove mappingqc.py - obsolete and superseded by bamstats.py

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• fixing errors

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• troubleshooting

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• troubleshooting

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Commits on Apr 25, 2022

• Removed realignment step as per GATK4

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• updated BSQR procedure to gatk4 syntax

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Commits on Apr 26, 2022

• Merge branch 'JS-current' into JS-exome

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Commits on May 4, 2022

• Gatk4 update: GVCF and GVCF database

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• Merge branch 'master' into JS-exome

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Commits on May 6, 2022

• gatk4: GenotypeGVCF now from database

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Commits on May 9, 2022

• added options for rMATS output filtering (results table) - FDR, PSI and coverage

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• options for pipeline splicing - yml file update

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• snpeff updated

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Commits on May 10, 2022

• bug corrections pipeline splicing

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• further bugfixes splicing pipeline

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• major changes exome pipeline

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Commits on May 11, 2022

• replace hapmap by somelier

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• remove xy prediction, which is provided by other tools and previous execution not ideal

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• Exome Pipeline Development

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Commits on May 12, 2022

• bugfixes exome pipeline:snpsift and revomal exomeancestry.py

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• snpsift bugfixes

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Commits on May 13, 2022

• Add SpliceAI

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Commits on May 16, 2022

• further exome pipeline - removed pedigree analysis

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• remove pedigree pipeline

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Commits on May 20, 2022

• functions to establish gene 'Panel' BED from list

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Commits on Mar 31, 2023

• various improvements to diff expression pipeline - able to handle unexpected data

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Commits on Sep 20, 2023

• Extensive changes to exome pipeline, bamstats and exploratory analysis

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• chages to exome.py

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Commits on Mar 30, 2024

• further development

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• addition of setup instruction for R tools

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• draft long read pipeline

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Commits on Dec 11, 2024

• Cchanges to cgatflow.py, compatibility with python 3.12

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• remove rpy2

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• add R scripts to new directory

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• add further R scripts, moved

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Commits on Dec 17, 2024

• Changes to Make GTFsubset compatible with sqlachemy changes

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• remove strand specificity which has been removed from cgat apps

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